Computer and Information SciencesBlogger

iPhylo

Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.
ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.
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Pensoft have recently introduced “nanopubs”, small structured publications that can be thought of as containing the minimum possible statement that could be published. Nanopubs are promoted as FAIR, that is findable, accessible, interoperabile, and reusable. I like the idea of nanopubs, but the examples I have seen so far are problematic.

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I’ve been down this road before, e.g. BHL, DjVu, and reading the f*cking manual and Demo of full-text indexing of BHL using CouchDB hosted by Cloudant, but I’m revisiting converting BHL page scans to black and white images, partly to clean them up, to make them closer to what a modern reader might expect, and partly to reduce the size of the image. The latter means faster loading times and smaller PDFs for articles.

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How to cite: Page, R. (2024). Hugging Face Autotrain https://doi.org/10.59350/7p1n4-wdv84 These are notes to myself on using Hugging Face AutoTrain. The first version of this had a very nice interface where you could simply upload a folder of images and train a model. It was limited in the range of tasks and models, but made up for that in ease of use.

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DataCite have released the Data Citation Corpus, together with a dashboard that summarises the corpus. This is billed as: The goal is to build a citation database between scholarly articles and data, such as datasets in repositories, sequences in GenBank, protein structures in PDB, etc. Access to the corpus can be obtained by submitting a form, then having a (very pleasant) conversation with DataCite about the nature of the corpus.

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How to cite: Page, R. (2023). It’s 2023 - why are we still not sharing phylogenies? https://doi.org/10.59350/n681n-syx67 A quick note to support a recent Twitter thread https://twitter.com/rdmpage/status/1729816558866718796?s=61&t=nM4XCRsGtE7RLYW3MyIpMA The article “Diversification of flowering plants in space and time” by Dimitrov et al. describes a genus-level phylogeny for 14,244 flowering plant genera.

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How to cite: Page, R. (2023). Where are the plant type specimens? Mapping JSTOR Global Plants to GBIF. https://doi.org/10.59350/m59qn-22v52 This blog post documents my attempts to create links between two major resources for plant taxonomy: JSTOR’s Global Plants and GBIF, specifically between type specimens in JSTOR and the corresponding occurrence in GBIF.

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How to cite: Page, R. (2023). Document layout analysis. https://doi.org/10.59350/z574z-dcw92 Some notes to self on document layout analysis. I’m revisiting the problem of taking a PDF or a scanned document and determining its structure (for example, where is the title, abstract, bibliography, where are the figures and their captions, etc.). There are lots of papers on this topic, and lots of tools.

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How to cite: Page, R. (2023). The problem with GBIF’s Phylogeny Explorer. https://doi.org/10.59350/v0bt3-zp114 GBIF recently released the Phylogeny Explorer, using legumes as an example dataset. The goal is to enables users to “view occurrence data from the GBIF network aligned to legume phylogeny.” The screenshot below shows the legume phylogeny side-by-side with GBIF data.